Variant report

Variant	rs277654
Chromosome Location	chr3:100043289-100043290
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:100036136..100038823-chr3:100040287..100043748,3	MCF-7	breast:
2	chr3:100042421..100044566-chr3:100070698..100073226,2	K562	blood:
3	chr3:100041368..100043333-chr3:100048533..100050924,3	MCF-7	breast:
4	chr3:100041336..100046382-chr3:100052282..100055066,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114021	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1036770	0.87[EUR][1000 genomes]
rs10936157	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs11915985	0.81[EUR][1000 genomes]
rs1214369	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1214372	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1214373	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12696064	1.00[ASN][1000 genomes]
rs12696084	0.95[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13070392	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs1609481	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs2028494	0.88[CEU][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs2029163	1.00[ASN][1000 genomes]
rs277636	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs277652	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35950794	1.00[ASN][1000 genomes]
rs3772698	0.88[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs4552390	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs4928119	0.88[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs4928169	0.88[CEU][hapmap];0.87[TSI][hapmap];0.88[EUR][1000 genomes]
rs62281675	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6763594	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6777265	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6802765	0.84[EUR][1000 genomes]
rs6808175	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7427443	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618677	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630257	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7637157	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7638503	0.84[EUR][1000 genomes]
rs9289985	1.00[CHD][hapmap];0.82[JPT][hapmap]
rs931332	0.84[EUR][1000 genomes]
rs967608	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs9854260	1.00[CHD][hapmap];0.82[JPT][hapmap]
rs9863738	1.00[CEU][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9875878	1.00[CHD][hapmap];0.82[JPT][hapmap]
rs9880795	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9882337	1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916476	chr3:99478229-100124625	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv1003924	chr3:99933762-100112690	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv869690	chr3:99984442-100054949	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs277654	TBC1D23	cis	Heart Left Ventricle	GTEx
rs277654	TBC1D23	cis	Muscle Skeletal	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:99980600-100053200	Weak transcription	Gastric	stomach
2	chr3:99996000-100052800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr3:99996000-100053000	Weak transcription	Small Intestine	intestine
4	chr3:100007000-100045000	Weak transcription	Lung	lung
5	chr3:100008600-100053000	Weak transcription	Aorta	Aorta
6	chr3:100009200-100045000	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr3:100015400-100053200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr3:100019600-100053000	Weak transcription	Colonic Mucosa	Colon
9	chr3:100020600-100053000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:100020600-100053000	Weak transcription	Hela-S3	cervix
11	chr3:100021800-100052800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr3:100021800-100053000	Weak transcription	Psoas Muscle	Psoas
13	chr3:100022000-100047600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:100022000-100052800	Weak transcription	Pancreas	Pancrea
15	chr3:100025800-100053000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:100025800-100053000	Weak transcription	Right Ventricle	heart
17	chr3:100026000-100052600	Weak transcription	Brain Hippocampus Middle	brain
18	chr3:100026000-100052800	Weak transcription	Thymus	Thymus
19	chr3:100026400-100045600	Weak transcription	HSMMtube	muscle
20	chr3:100026400-100052800	Weak transcription	NHEK	skin
21	chr3:100026400-100053000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:100026600-100048600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr3:100026600-100052800	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:100029600-100053000	Weak transcription	Brain Substantia Nigra	brain
25	chr3:100030200-100049800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr3:100030200-100053000	Weak transcription	Fetal Brain Female	brain
27	chr3:100031000-100053000	Weak transcription	Rectal Smooth Muscle	rectum
28	chr3:100031200-100051200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:100033200-100046600	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr3:100033600-100044600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr3:100033600-100045000	Weak transcription	Fetal Stomach	stomach
32	chr3:100033600-100052800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr3:100034800-100046600	Strong transcription	HSMM	muscle
34	chr3:100035000-100053000	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr3:100035600-100053000	Weak transcription	Stomach Mucosa	stomach
36	chr3:100036000-100052400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr3:100036000-100053000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr3:100036200-100046600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr3:100036200-100047400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:100036200-100052800	Weak transcription	A549	lung
41	chr3:100036200-100053000	Weak transcription	Colon Smooth Muscle	Colon
42	chr3:100036400-100046000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:100036600-100046600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr3:100037000-100053000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:100037400-100053000	Weak transcription	GM12878-XiMat	blood
46	chr3:100038400-100045000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr3:100038800-100053000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr3:100039000-100053000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr3:100039000-100053000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr3:100039200-100053000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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